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   <div id="projectname">NINJA
   &#160;<span id="projectnumber">2.x</span>
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<div class="contents">
<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>

<h3><a id="index_a"></a>- a -</h3><ul>
<li>A
: <a class="el" href="class_array_heap_ext_mem.html#a352c27df70ca0deac7b053bafc5b775f">ArrayHeapExtMem</a>
, <a class="el" href="class_distance_calculator.html#a00bdfa4cc790ce19056cf06894e205f4">DistanceCalculator</a>
</li>
<li>aa_chars
: <a class="el" href="class_distance_calculator.html#a721cb1b004a4d856515be5b8c4fc0fc4">DistanceCalculator</a>
</li>
<li>alignment
: <a class="el" href="class_argument_handler.html#ae693a55bec1ed6005f0976a40a7f854aafe3d262ec86ee31ed3d27ef42b1f235a">ArgumentHandler</a>
, <a class="el" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68a5496170f117c3d558853e10ccee02666">TreeBuilderManager</a>
</li>
<li>alph_type
: <a class="el" href="class_distance_calculator.html#a7d15fa02f8da2455998c97b3c18d0bc0">DistanceCalculator</a>
</li>
<li>AlphabetType
: <a class="el" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87">ArgumentHandler</a>
, <a class="el" href="class_distance_calculator.html#aba37861b27b2e9a8e12b0aea4fcb5c7c">DistanceCalculator</a>
, <a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7">SequenceFileReader</a>
, <a class="el" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008">TreeBuilderManager</a>
</li>
<li>alphType
: <a class="el" href="class_sequence_file_reader.html#a9318592fe459d2b67d3fb191b1f75057">SequenceFileReader</a>
, <a class="el" href="class_tree_builder_manager.html#a3047ef12674cd2feab230d5445ec057e">TreeBuilderManager</a>
</li>
<li>amino
: <a class="el" href="class_argument_handler.html#ac2a6552abc7c6449b625791aefdf6d87abf0a7e58c2a951cb200e05ceed789d48">ArgumentHandler</a>
, <a class="el" href="class_distance_calculator.html#aba37861b27b2e9a8e12b0aea4fcb5c7cad0f2f6fb9391cbe99f3f7b9dc4cfd63a">DistanceCalculator</a>
, <a class="el" href="class_sequence_file_reader.html#a8cc42e15f26ed4a680ac4b968f0922a7acae42440ed46d49841a42325c14aaf41">SequenceFileReader</a>
, <a class="el" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008a089be0a828fca4605323da2e3a171202">TreeBuilderManager</a>
</li>
<li>ArgumentHandler()
: <a class="el" href="class_argument_handler.html#a2657983b12529181db92512d3a6fc1fa">ArgumentHandler</a>
</li>
<li>argumentTest()
: <a class="el" href="class_argument_handler.html#aed3ea207ece08d71c49613911ac8b711">ArgumentHandler</a>
</li>
<li>ArrayHeapExtMem()
: <a class="el" href="class_array_heap_ext_mem.html#a6a94015ca871c8b85a56b90d935aa276">ArrayHeapExtMem</a>
</li>
<li>arrayHeaps
: <a class="el" href="class_tree_builder_ext_mem.html#acb9a7c738ae2fbbd270c04b91d63cdb4">TreeBuilderExtMem</a>
</li>
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